Crystal Structure of Cindoxin, Surface Entropy reduction Mutant

Experimental Data Snapshot

  • Resolution: 1.21 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

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Crystal structure of cindoxin, the P450cin redox partner.

Madrona, Y.Hollingsworth, S.A.Tripathi, S.Fields, J.B.Rwigema, J.C.Tobias, D.J.Poulos, T.L.

(2014) Biochemistry 53: 1435-1446

  • DOI: https://doi.org/10.1021/bi500010m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the flavin mononucleotide (FMN)-containing redox partner to P450cin, cindoxin (Cdx), has been determined to 1.3 Å resolution. The overall structure is similar to that of the FMN domain of human cytochrome P450 reductase. A Brownian dynamics-molecular dynamics docking method was used to produce a model of Cdx with its redox partner, P450cin. This Cdx-P450cin model highlights the potential importance of Cdx Tyr96 in bridging the FMN and heme cofactors as well P450cin Arg102 and Arg346. Each of the single-site Ala mutants exhibits ~10% of the wild-type activity, thus demonstrating the importance of these residues for binding and/or electron transfer. In the well-studied P450cam system, redox partner binding stabilizes the open low-spin conformation of P450cam and greatly decreases the stability of the oxy complex. In sharp contrast, Cdx does not shift P450cin to a low-spin state, although the stability of oxy-P450cin is decreased 10-fold in the presence of Cdx. This indicates that Cdx may have a modest effect on the open-closed equilibrium in P450cin compared to that in P450cam. It has been postulated that part of the effector role of Pdx on P450cam is to promote a significant structural change that makes available a proton relay network involving Asp251 required for O2 activation. The structure around the corresponding Asp in P450cin, Asp241, provides a possible structural reason for why P450cin is less dependent on its redox partner for functionally important structural changes.

  • Organizational Affiliation

    Departments of †Molecular Biology and Biochemistry, ‡Chemistry, and §Pharmaceutical Sciences, University of California , Irvine, California 92697-3900, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cindoxin162Citrobacter braakiiMutation(s): 3 
Gene Names: cinC
Find proteins for Q8VQF4 (Citrobacter braakii)
Explore Q8VQF4 
Go to UniProtKB:  Q8VQF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VQF4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FMN

Download Ideal Coordinates CCD File 
C17 H21 N4 O9 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.21 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.109α = 90
b = 82.109β = 90
c = 37.042γ = 120
Software Package:
Software NamePurpose

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM33688

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Refinement description